I had same issue.
According to this:http://stackoverflow.com/questions/6382330/does-this-php-code-crash-apac...
you should decrease value of pcre.backtrack_limit .
I set it to 500, and it didn't crash.
For some reason now I get following error after this:Notice: Undefined offset: 1 in module_builder_update_documentation() (line 82)
and module builder doesn't build any hooks except of hook_help. But at least update doesn't crash php.